GraphOnlyFingerprinter.java

/* $Revision: 7673 $ $Author: egonw $ $Date: 2007-01-09 10:39:35 +0100 (Tue, 09 Jan 2007) $ * * Copyright (C) 2002-2007 Egon Willighagen <egonw@users.sf.net> * * Contact: cdk-devel@lists.sourceforge.net * * This program is free software; you can redistribute it and/or * modify it under the terms of the GNU Lesser General Public License * as published by the Free Software Foundation; either version 2.1 * of the License, or (at your option) any later version. * All we ask is that proper credit is given for our work, which includes * - but is not limited to - adding the above copyright notice to the beginning * of your source code files, and to any copyright notice that you may distribute * with programs based on this work. * * This program is distributed in the hope that it will be useful, * but WITHOUT ANY WARRANTY; without even the implied warranty of * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the * GNU Lesser General Public License for more details. * * You should have received a copy of the GNU Lesser General Public License * along with this program; if not, write to the Free Software * Foundation, Inc., 51 Franklin St, Fifth Floor, Boston, MA 02110-1301 USA. */package org.openscience.cdk.fingerprint;
import java.util.BitSet;
import java.util.Iterator;
import java.util.Map;
import java.util.Random;
import org.openscience.cdk.interfaces.IAtomContainer;
/** * Specialized version of the Fingerprinter which does not take bond orders * into account. * * @author egonw * @cdk.created 2007-01-11 * @cdk.keyword fingerprint * @cdk.keyword similarity * @cdk.module standard * * @see org.openscience.cdk.fingerprint.Fingerprinter */00046publicclass GraphOnlyFingerprinterextendsFingerprinter {
/** * Creates a fingerprint generator of length <code>defaultSize</code> * and with a search depth of <code>defaultSearchDepth</code>. */00052publicGraphOnlyFingerprinter() {
super(defaultSize, defaultSearchDepth);
}
publicGraphOnlyFingerprinter(int size) {
super(size, defaultSearchDepth);
}
publicGraphOnlyFingerprinter(int size, int searchDepth) {
super(size, searchDepth);
}
/** * Gets the bondSymbol attribute of the Fingerprinter class. Because we do * not consider bond orders to be important, we just return ""; * * @param bond Description of the Parameter * @return The bondSymbol value */00071protected String getBondSymbol(org.openscience.cdk.interfaces.IBond bond) {
return"";
}
protected BitSet getFingerprint(IAtomContainer ac, int size) throws Exception {
Map paths = findPathes(ac, super.getSearchDepth());
BitSet bs = new BitSet(size);
for (Iterator e = paths.values().iterator(); e.hasNext(); ) {
bs.set(new Random(((String)e.next()).hashCode()).nextInt(size));
}
return bs;
}
}